NEED SERIOUS OBDII HELP...

I've done that before. Obviously when I load the stock tune, It sets the MIL light for O2 Sensors and Heater. They are there and working, but the Long Tubes and Catback set it off.

What codes do you get exactly, when you load the stock tune back on? The longtubes and catback shouldn't have anything to do with a MIL, but I could see it throwing a code for the downstream O2 sensors if you have no cats, or if the downstream O2 sensors are somehow turned off in the tune. Knowing the codes with the stock tune is really the key here to finding a solution to the issues you're experiencing. You may have a hard fault of some sort, which the tune is changing parameters and ignoring a fault condition.
 
All tunes I have tried have the O2 sensors turned on. With the stock tune, I get the following codes: P0155 and P0161. I know they relate to the O2 sensors and Circuits. This is only with the stock tune. The JDM and Bama tunes were verified (O2's On), but they dont throw any codes. Just doesn't complete.
 
you say you have long tubes,,,i had a problem with mine...we added to the harness the old way with adding wire....than we used new o2`s with the longer harness,,and now no codes...


when you install the stock tune,,with key on engine off do the o2 heaters come on? feel o2 it should get very hot with just key on
 
JDM Fixed it !! - All, listen to this. I brought the car to Jim at JDM Engineering. He verified that all of the sensors were working, cats are there, etc.. They were unsure what was causing the issue, but did say that the JBA headers were "Very" Long. He modified the tune to increase the monitor temp of the rear O2 sensor. We loaded the tune and he hooked the car up to more monitoring gear. We ran the car for about an hour (not moving), but the same 3 monitors still said inc. He suggested that I put some miles on the car and maybe stop back to check again. I left and while I was driving, hooked up my OBD Scanner. After 3 miles, the O2 Monitor and O2 Heater Monitor went green (complete). I couldn't believe it. I drove straight to the NJ State Inspection Center. The Inspector Immediately opened the hood for a look, but went on with the inspection. GOT MY STICKER !! It Passed !! I have to say if you guys need a real pro and expert in stangs, go to JDM. They are unbelievable and great guys to work with. Thanks to all for your suggestions !! JDM is the BEST ...